Difference between revisions of "PfamScan"

From UFRC
Jump to navigation Jump to search
(Created page with "Category:SoftwareCategory:BioinformaticsCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|pfamscan}} |{{#vardefine:url|http://ftp.ebi.ac.uk/pub/...")
 
 
(6 intermediate revisions by 3 users not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+
[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|pfamscan}}
 
|{{#vardefine:app|pfamscan}}
Line 5: Line 5:
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
Line 19: Line 19:
  
 
Search a FASTA file against a library of Pfam HMMs
 
Search a FASTA file against a library of Pfam HMMs
 
Note that on our system the pfamscan module is an alias for the [[HMMER3|hmmer]] module as we installed pfamscan within hmmer.
 
  
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
===Serial===
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 44: Line 32:
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
  
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+
On our system the pfamscan module is an alias for the [[HMMER3|hmmer]] module as we installed pfamscan within hmmer.
 +
 
 +
You don't have to provide the '-dir' argument to the pfam_scan.pl command as we configured it to use the default location of the most current Pfam reference data release at '<code>/data/reference/reference/pfam/current/</code>'.
  
 
|}}
 
|}}

Latest revision as of 20:19, 12 August 2022

Description

pfamscan website  

Search a FASTA file against a library of Pfam HMMs

Environment Modules

Run module spider pfamscan to find out what environment modules are available for this application.

System Variables

  • HPC_PFAMSCAN_DIR - installation directory

Additional Information

On our system the pfamscan module is an alias for the hmmer module as we installed pfamscan within hmmer.

You don't have to provide the '-dir' argument to the pfam_scan.pl command as we configured it to use the default location of the most current Pfam reference data release at '/data/reference/reference/pfam/current/'.



Citation

If you publish research that uses pfamscan you have to cite it as follows:

The Pfam protein families database: R.D. Finn, A. Bateman, J. Clements, P. Coggill, R.Y. Eberhardt, S.R. Eddy, A. Heger, K. Hetherington, L. Holm, J. Mistry, E.L.L. Sonnhammer, J. Tate, M. Punta Nucleic Acids Research (2014) Database Issue 42:D222-D230